RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GuWtHh/RM_908679.SatMar161326062024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1710620765 Database = /dev/shm/rModeler.GuWtHh/GCA_036013445.1_bCalNic1.hap1 - Sequences = 807 - Bases = 1285851275 - N50 = 110148392 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202003808-216431472 | [ 1 ] 187576145-202003808 | [ ] 173148481-187576144 | [ ] 158720818-173148481 | [ 1 ] 144293155-158720818 | [ ] 129865491-144293154 | [ ] 115437828-129865491 | [ 1 ] 101010164-115437827 | [ 1 ] 86582501-101010164 | [ ] 72154838-86582501 | [ 1 ] 57727174-72154837 | [ 1 ] 43299511-57727174 | [ ] 28871847-43299510 | [ 3 ] 14444184-28871847 | [ 8 ] 16521-14444184 |************************************************** [ 790 ] Storage Throughput = excellent ( 1227.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000461 bp ( 40000461 non ambiguous ) - Num Contigs Represented = 132 - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:55 (hh:mm:ss) Elapsed Time Round Time: 00:24:56 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2283 repeats masked totaling 823395 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029896 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10029896 bp After Masking: 8589769 bp Masked: 14.36 % -- Input Database Coverage: 10029896 bp out of 1285851275 bp ( 0.78 % ) Sampling Time: 00:04:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:06:15 (hh:mm:ss) Elapsed Time, 331 HSPs Collected Number of families returned by RECON: 192 Round Time: 00:10:35 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7099 repeats masked totaling 2782165 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010540 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 30010540 bp After Masking: 24355875 bp Masked: 18.84 % -- Input Database Coverage: 40040436 bp out of 1285851275 bp ( 3.11 % ) Sampling Time: 00:18:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:31:07 (hh:mm:ss) Elapsed Time, 5015 HSPs Collected Number of families returned by RECON: 1165 Round Time: 00:49:37 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:44:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21885 repeats masked totaling 7801131 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034892 bp Num Contigs Represented = 213 Non ambiguous bp: Initial: 90033304 bp After Masking: 74899583 bp Masked: 16.81 % -- Input Database Coverage: 130075328 bp out of 1285851275 bp ( 10.12 % ) Sampling Time: 00:49:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 03:41:25 (hh:mm:ss) Elapsed Time, 188877 HSPs Collected Number of families returned by RECON: 7423 Round Time: 04:38:25 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:19:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 78047 repeats masked totaling 28178271 bp(s). - TE Masking time 00:03:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015971 bp Num Contigs Represented = 431 Non ambiguous bp: Initial: 270011000 bp After Masking: 219641124 bp Masked: 18.65 % -- Input Database Coverage: 400091299 bp out of 1285851275 bp ( 31.11 % ) Sampling Time: 02:36:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23368866 Comparison Time: 26:46:50 (hh:mm:ss) Elapsed Time, 1082557 HSPs Collected Number of families returned by RECON: 46490 Round Time: 29:57:36 (hh:mm:ss) Elapsed Time : 223 families discovered. RepeatScout/RECON discovery complete: 413 families found Classification Time: 00:30:06 (hh:mm:ss) Elapsed Time Program Time: 36:31:15 (hh:mm:ss) Elapsed Time